When you may use functions of 3 or more arguments, it becomes trivial to find a single function that can be used to express large classes of other functions.
These tricks break when you are restricted to use one binary function, like in the EML paper.
The second argument cannot be used as a selector, because you cannot make binary functions from unary functions (while from binary functions you can make functions with an arbitrary number of parameters, by composing them in a tree).
If you used an argument as a function selector in a binary function, which transforms the binary function into a family of unary functions, then you would need at least one other auxiliary binary function, to be able to make functions with more than one parameter.
The auxiliary binary function could be something like addition or subtraction, or at the minimum a function that makes a tuple from its arguments, like the function CONS of LISP I.
The EML paper can also be understood that the elementary functions as defined by it can be expressed using a small family of unary functions (exponential, logarithmic and negation), together with one binary function: addition.
Then this set of 4 simple functions is reduced to one complex function, which can regenerate any of those 4 functions by composition with itself.
This is the same trick used to reduce the set of 2 simple functions, AND & NOT, which are sufficient to write any logical function, to a single function, NAND, which can generate both simpler functions.